Lecture 01 Administrative issues What is Genetics? Course outline

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1 Lecture 01 Administrative issues What is Genetics? Course outline Lecture 02 Protein function Relationship to phenotype Specific binding and non-covalent forces Protein structure Amino acids Peptide bonds Secondary structure α-helix β-pleated sheet Tertiary structure R groups and forces Quaternary structure Lecture 03 Introduction to nucleic acid function DNA structure Deoxyribonucleotides Phosphodiester bonds Double helix Complementary base pairing Higher order structure RNA structure Ribonucleotides Stem and loop structures Higher order structure Complementary base pairing and function Lecture 04 Outline of gene expression The genetic code Introduction to transcription RNA polymerases Initiation, elongation, and termination Gene classes Transcription initiation in prokaryotes RNA polymerase σ subunits Promoters Regulatory proteins

2 Lecture 05 Transcription termination in prokaryotes ρ independant ρ dependant Transcription initiation in eukaryotes RNA polymerases I and III RNA polymerase II General transcription factors and core promoters Additional transcription factors, proximal promoters, and enhancers Regulation Transcription termination in eukaryotes RNA polymerases I and III RNA polymerase II Lecture 06 Processing in prokaryotes For rrna For trna For mrna Processing in eukaryotes For rrna For trna For mrna Capping Polyadenylation Splicing Alternative splicing Lecture 07 Introduction to translation trna function Ribosomes Initiation, elongation, and termination Translation in prokaryotes Ribosomes Initiation, elongation, and termination Translation factors Lecture 08 Translation in eukaryotes Ribosomes Initiation, elongation, and termination Translation factors

3 Lecture 09 Introduction to DNA replication Origins, semiconservative, bidirectional DNA polymerases 5 to 3 polymerase, 3 to 5 proofreading exonuclease, primers Replication in prokaryotes Initiation and elongation Replisomes Linking Okazaki fragments Replication in eukaryotes Initiation Elongation Lecture 10 Chromatin components DNA, proteins, RNA Histones 10nm fibre Nucleosome Domains and territories Scaffold/matrix and loops Interphase and M phase Chromosomes Unreplicated and replicated Telomeres and centromere Metacentric, acrocentric, and telocentric Lecture 11 Binary fission Cell cycle M, G1, S, G2 phases Mitotic cell division Mitosis and cytokinesis Overview, stages, functions Sexual reproduction Haploid, diploid, alleles, homologous pairs Meiotic cell division Overview, stages, functions Life cycles Typical haploid, typical diploid

4 Lecture 12 Single gene cross, haploid adult Worked example based on meiosis Single gene cross, diploid adult Homozygous and heterozygous Allele interactions Dominant and recessive Incompletely dominant Codominant Molecular basis for above interactions Worked examples based on meiosis Homozygous dominant x homozygous recessive Heterozygous x heterozygous Lecture 13 Monohybrid crosses Gene and allele symbols, slash notation Extensions to monohybrid crosses Multiple alleles Examples Recessive lethals No pure breeding lines, ratios Sex linkage Sex chromosomes, homogametic and heterogametic sexes Inheritance patterns for X-linked genes Hemizygosity, dosage compensation Alternative mechanisms for sex determination Lecture 14 Dihybrid crosses Unlinked and linked Crosses with unlinked loci Gametes depend on chromosome alignment Parental and recombinant type gametes 50% parental, 50% recombinant Forked-line method Interactions between loci Dominant epistasis Recessive epistasis Others

5 Lecture 15 Gamete formation with linked loci Gametes depend on crossing over If no crossing over occurs between loci in a meiosis 100% parental, 0% recombinant If crossing over occurs between loci in a meiosis 50% parental, 50% recombinant Frequency of meioses with crossing over determines recombinant percentage What determines frequency of meioses with crossing over between loci? Physical distance between loci Large distance, high frequency of crossing over Small distance, low frequency of crossing over Lecture 16 Genetic mapping Use percentage of recombinant gametes to map gene loci Test crosses Double heterozygote crossed with double homozygous recessive Progeny phenotypes reflect gamete genotypes from double heterozygote Double homozygous recessive is unimportant Gene nomenclature (fruit flies) Gene named after abnormal phenotype Abnormal phenotype dominant: gene name, symbol begin with upper case Abnormal phenotype recessive: gene name, symbol begin with lower case Normal (wild type) allele is given a superscript plus Abnormal allele is not Lecture 17 Example test cross Percentage recombinants is the map distance Coupling and repulsion Errors result in map distances above 50% More than one crossover between loci Two, three, and four strand double crossovers Average out at 50% recombinants Hence one or more crossovers gives 50% recombinants Mapping function As separation increases, measured map distance approaches 50% Short distances add up, long distances do not Use of χ 2 test to distinguish unlinked and linked loci

6 Lecture 18 Mutation Gene and chromosome Types of gene mutation Substitutions Transitions and transversions Indels Causes of gene mutation Spontaneous Tautomers, deamination, depurination, miss-paired repeats Induced Base analogues, base modifiers, intercalating agents Ultraviolet light, thymine, high energy radiation Lecture 19 Effects on gene function Coding regions Silent, missense, nonsense, frameshift Non-coding regions Reversions and suppressors Exact and equivalent reversions Intragenic and extragenic suppressors Frame shift and nonsense Organismal effects Morphological, behavioral, lethal, nutritional, conditional Penetrance and expressivity Complementation test Lecture 20 Chromosome identification Deletions Recessive lethal, hemizygosity, suppressed recombination Duplications Inversions Paracentric and pericentric Altered linkage map (homozygous), suppressed recombination (heterozygous) Reciprocal translocations Cross shapes (heterozygous), altered linkage maps, reduced fertility (heterozygous) Abnormal euploidy Even n fertile, odd n sterile Aneuploidy

7 Lecture 21 Continuous variation Genetic basis for continuous variation Multiple alleles Polygenic inheritance Environmental effects Identifying loci QTL mapping GWA studies Uses Medical applications Lecture 22 Definitions Population, gene pool Describing the gene pool Genotype frequency, allele frequency Does sexual reproduction alter the gene pool? Hardy-Weinberg equilibrium Assumptions: two alleles, random mating, infinite population Conclusions: gene pool unchanged, genotypes in fixed ratio Applications of Hardy-Weinberg equilibrium Determine allele frequencies in dominant-recessive situation Determine whether population is in Hardy-Weinberg equilibrium Lecture 23 Mechanisms that change the gene pool Mutation Creates and eliminates alleles Equilibrium reached slowly Selection Genotype affects probability of having offspring Fertility, survival, attractiveness Relative fitness Modified Hardy-Weinberg equation Frequency-independant selection Heterozygote has intermediate fitness, highest fitness, lowest fitness Frequency-dependant selection

8 Lecture 24 Mechanisms that change the gene pool (continued) Genetic drift Random events may affect finite populations Most relevant in small populations Bottleneck and founder effects Gene flow Mating between populations Depends on amount of mating and difference in gene pools Sources of Variation Quantifying variation Percentage of polymorphic loci Average heterozygosity Lecture 25 Use of nutritional mutations Methods for making partial diploids Transformation Uses DNA Fate of DNA: recombination or degradation Plasmids Mapping by cotransformation Conjugation F factor Integration and excision F-, F+, Hfr, and F' states Rolling circle replication

9 Lecture 26 Methods for making partial diploids (continued) Conjugation (continued) Transfer using F+, Hfr, and F' donors Frequency of host gene and F factor transfer Mapping by time of gene transfer Transduction Bacteriophage structure Lytic life cycle Lysogenic life cycle Virulent and temperate bacteriophage Generalized transduction Specialized transduction Lecture 27 Applications of recombinant DNA technology Principles of recombinant DNA technology Complementary base pairing Use of enzymes of DNA metabolism DNA polymerases Restriction enzymes DNA ligases Reverse transcriptases Chemical synthesis Uses DNA detection PCR DNA sequencing Dideoxy method and massively parallel sequencing Lecture 28 Uses (continued) Characterization of genes Gene structure and transcript variants RT-PCR Reporter genes Transfer of specific sequences Cloning Manipulation of genes and gene expression RNAi Ectopic expression in vitro mutagenesis CRISPR and homology directed repair Gene therapy

10 Lecture 29 Examples Cloning of human insulin gene Gene assembly from oligonucleotides Directional cloning Modelling cancer and cancer therapies Gene activation by Cre recombinase Gene activation by doxycycline Evolution of limblessness in snakes CRISPR editing of ZRS enhancer Environmental DNA and fisheries management edna Comparison with electrofishing Lecture 30 Definition of genomics Functional genomics Comparative genomics Repeated sequences Dispersed Retrotransposons, DNA transposons Tandem array Telomeres, centromeres, rdna Unique sequences Coding sequences mrna (exons vs introns), small RNAs Minimum genome size Ape vs human comparisons Lecture 31 Reasons for gene regulation Efficient use of resources, tissue-specific expression Levels of gene regulation Transcription, processing, translation Regulation at transcription (prokaryotes) Alternate sigma subunits Activators and repressors Structure of Lac operon Polycistronic RNA, coordinate regulation Roles of Lac repressor, CRP Mutations in lac Z, Y, A, promoter, operator Partial diploids: cis-acting mutations

11 Lecture 32 Regulation at transcription (continued) Mutations in laci Partial diploids: trans-acting mutations Regulation at translation (prokaryotes) Regulation at transcription (eukaryotes) Transcription factors, enhancers, etc. Chromatin structure Open vs closed, DNA methylation, histone modification Lecture 33 Regulation at processing (eukaryotes) Alternate splicing Regulation at translation (eukaryotes) mirnas Synthesis and function